I am searching for an answer to this question as well. What kind of pump is the most gentle? Have you made progress in answering it? Did you try that 12v pump (12 volt on-demand diaphragm pump 1 GPM 40 PSI) from Northern Tool?

My guess is that a "small electric pump" (presumably not centrifugal) would be fine for species of algae used for biodiesel (single organ-entities and 10 microns or smaller). An electric pump such as a common continuous-duty pond pump might just be like a super-fast water ride for them.

That is just a guess. It would be great if people who actually had experience would let us know.

I found an answer. The answer is that DIAPHRAGM PUMPS are the most gentle. This animated GIF makes it pretty clear why they are so gentle. http://en.wikipedia.org/wiki/File:DiaphragmPump.gif I cannot imagine that a diaphragm pump would ever harm non-strand-forming, small diameter algae. All the pump does is apply a negative pressure and a positive pressure. The algae just go through two gates. And that's it. A centrifugal pump, however, should probably be avoided, though perhaps such algae would not even be harmed by such pumps because they are so small. You would just have to try and see.